[Bioperl-l] Bio::SearchIO TFASTX parsing bug

Daniel Mascarenhas danielmt at fiocruz.br
Tue Oct 19 11:06:57 EDT 2004


we've been using $hit->logical_length('query') on TFASTX reports and 
noticed that it corresponds to $result->query_length divided by 3. That 
is exactly what we would expect  for TBLASTX, where both the query and 
hit sequences are translated into aminoacid sequences, however, TFASTX 
compares a protein sequence to a DNA sequence database and therefore 
just the hit logical length makes sense. So, everything else that 
depends on the $hit->logical_length('query') is miscalculated.

We're using bioperl-live from cvs (updated almost daily).


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